Salil Shetty is no stranger to radicalism: his father was a campaigning journalist and his mother a feminist activist. Now, as the new secretary general of Amnesty International, he is in charge of the world's largest, most liberal human rights organisation.

Speaking to the Observer in his first interview since taking up his new role last month, Shetty said: "My father was a journalist and my mother was active in the women's movement in Bangalore. Our phone was tapped and my dad was arrested many times." Growing up in India in the tumultuous 1970s, he lived through the 1976 state of emergency which led to human rights being curtailed and an intense level of activism. "I was president of the student union in Bangalore, and the lesson I learnt was that the root of injustice is people who have captured power abusing it – and holding those people to account is what Amnesty is all about."

Shetty, who came to Amnesty after seven years as director of the UN Millennium Campaign and five years at ActionAid, is the first Indian to lead Amnesty. His first weeks have not been free of controversy, and some of the rows have been with competing liberal voices. Last week Amnesty and four other human rights organisations wrote to the whistleblowing website WikiLeaks, urging it to remove thousands of names from the leaked Afghanistan war logs which it posted last month. Amnesty argues that a failure to edit the names could inspire a surge in assassinations by the Taliban. The founder of WikiLeaks, Julian Assange, replied by asking the groups concerned to help WikiLeaks edit the names. He also threatened to expose Amnesty if it refused to provide staff to help with the task.

Shetty told the Observer: "Digital media offers so much potential to expose human rights violations and as a platform for change, but with these new opportunities the responsibility to do no harm remains paramount. The protection of civilians will always be Amnesty's priority. That is why, along with other human rights groups, we are involved in a dialogue with WikiLeaks."

The discussion with WikiLeaks is both an example of how the number of players in the field of human rights has increased with the emergence of digital media and also of the challenges facing Amnesty in negotiating this new world. Shetty said that the presence of WikiLeaks only served to highlight the critical role Amnesty can play in verification and processing raw data.

Shetty has also become involved in another clash over the organisation's liberal agenda. The closure of the Guantánamo Bay detention camp, promised by Barack Obama while a presidential candidate but not yet fulfilled, is still an Amnesty goal, and Shetty says the organisation will continue to push hard on releasing the detainees.

The relationship between some of those campaigning for Guantánamo's closure and Amnesty has been the source of some controversy. Gita Sahgal, the head of Amnesty's gender unit, resigned this year after accusing the organisation of ideological bankruptcy and misogyny. Sahgal was particularly critical of Amnesty's links with Moazzam Begg, a former inmate at Guantánamo Bay, and his group Cageprisoners, and said this support was undermining its campaign for women's rights.

The Begg affair earned some negative headlines for Amnesty, but Shetty puts forward a robust defence of its position. "If a woman is dying I don't first ask what are your views about the Taliban," he said. "If we start choosing which prisoner of conscience we support, depending on their views about the world as a whole, that goes against the idea that a right to life is a fundamental human right."

The idea of human rights being universal is something Shetty imbibed early in his life and he believes that being Indian can be useful in making that argument. "If you ask poor people in developing countries or countries like India, where I am from, about whether human rights are a western concept they would not even understand the question," he said. "The popular misconception is that human rights are something that is given from the west to developing countries. But my take is different, and for me the idea of basic human rights – the right to education, free expression – is deeply embedded."

The challenge for Amnesty lies, he believes, in making the organisation truly international. "Our presence in the developing world needs to expand," he said. "We need a more vibrant presence in India, Brazil and Africa so that it is the people there who are doing the research and the campaigning and not people sitting in London." Amnesty International's origins, from its inception following a letter in the Observer in 1961, were linked to the idea of individual members making a difference.

"One of the biggest attractions that drew me to come into the Amnesty International fold is the membership of 2.8 million members who are able to push from the bottom," he said. "If that didn't exist, then one of the most powerful rationales for its legitimacy would be weakened, so that is at the heart of my interest because Amnesty has a unique ability to speak truth to power."

Next year Amnesty, like Shetty, will turn 50. "There has been a decreasing level of trust in our political leaders and more recently there has been a corresponding lack of trust in corporate leaders," he said. "In that context, organisations like Amnesty are even more important because we are still trusted, since everyone knows we don't have any axe to grind – so the job of shining a light on injustice and human rights violation has never been more important."